Why is this hair particle system not properly into account the 'density' vertex group?
You should use the Weight Paint mode to create your vertex group.
Make sure you Apply Transforms on your mesh aswell.

Regarding "separating part", creating 'scalps', I think it is a better way to go especially when using animated characters. 



Post a blend file if you still struggle.

EDIT: The Particle tool has a known bug when used with subdivision surfaces, and Multires. So it's "normal" and is being solved.
(SOURCE: https://soundcloud.com/blender-institute/podcast-ep-006-flexirig @ 12:50mn)